8CWJ: Fab arms of antibodies 4C12-B12 and CR3022

Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin receptor binding domain (pRBD). Determined by X-ray diffraction at 2.45 Å resolution. Released 24 May 2023.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Homo sapiens, Pangolin coronavirus
Chains: 10
Atoms: 16,808
Mol. weight: 242.85 kDa
Ligands: NAG
Released: 24 May 2023

Explore 8CWJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CWJ contains 72 α-helices and 213 β-strands across 10 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	18
β-strand	10-12	3	19
β-strand	18-26	9	18
α-helix	29-31	3
β-strand	33-39	7	19
β-strand	46-52	7	19
β-strand	57-60	4	19
β-strand	69-73	5	18
α-helix	74-76	3
β-strand	78-83	6	18
α-helix	88-90	3
β-strand	92-99	8	19
β-strand	102	1	20
β-strand	108-109	2	19
β-strand	113-117	5	19
β-strand	123	1	21
α-helix	124-125	2
β-strand	126-130	5	22
α-helix	131-133	3
β-strand	142-151	10	22
β-strand	152	1	21
β-strand	157-160	4	23
β-strand	165	1	23
β-strand	170-171	2	22
α-helix	172-174	3
β-strand	175-176	2	22
β-strand	182-190	9	22
β-strand	201-206	6	23
α-helix	207-209	3
β-strand	211-216	6	23

Chain B: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-13	4	25
β-strand	19-25	7	24
β-strand	30-31	2	26
β-strand	36-37	2	26
β-strand	39-44	6	25
β-strand	51-55	5	25
β-strand	59-60	2	25
α-helix	61	1
β-strand	68-73	6	24
β-strand	76-81	6	24
α-helix	86-88	3
β-strand	90-96	7	25
α-helix	102	1
β-strand	103-104	2	25
β-strand	108-112	5	25
β-strand	117	1	27
β-strand	120-124	5	28
α-helix	125-127	3
α-helix	128-131	4
β-strand	135-145	11	28
β-strand	146	1	27
β-strand	151-156	6	29
β-strand	165-169	5	28
α-helix	171-173	3
β-strand	179-188	10	28
β-strand	197-203	7	29
β-strand	211-216	6	29

Chain G: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	334	1
β-strand	335	1	13
α-helix	336	1
α-helix	338-342	5
α-helix	347-348	2
β-strand	349	1	3
β-strand	354-358	5	3
β-strand	361-362	2	13
α-helix	366-369	4
β-strand	376-380	5	3
α-helix	384-389	6
β-strand	391-392	2	13
β-strand	394-403	10	3
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	3
α-helix	439-442	4
β-strand	448	1	14
β-strand	452-454	3	15
α-helix	460-462	3
β-strand	469	1	16
α-helix	471-472	2
β-strand	473-474	2	17
β-strand	485	1	17
β-strand	488-489	2	17
β-strand	492-494	3	15
β-strand	497	1	14
α-helix	503-505	3
β-strand	507-516	10	3
β-strand	524-525	2	13

Chain H: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	10-12	3	2
β-strand	18-26	9	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	46-52	7	2
β-strand	57-60	4	2
β-strand	69-73	5	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	102	1	3
β-strand	108-109	2	2
β-strand	113-117	5	2
β-strand	123	1	4
β-strand	126-130	5	5
α-helix	131-133	3
β-strand	144-151	8	5
β-strand	152	1	4
β-strand	157-160	4	6
β-strand	169-171	3	5
α-helix	172-174	3
β-strand	175-176	2	5
β-strand	182-188	7	5
β-strand	201-206	6	6
α-helix	207-209	3
β-strand	211-216	6	6

Chain I: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	335	1	30
α-helix	338-342	5
β-strand	349	1	20
β-strand	354-358	5	20
β-strand	361-362	2	30
α-helix	366-369	4
β-strand	376-380	5	20
α-helix	384-389	6
β-strand	391-392	2	30
β-strand	394-403	10	20
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	20
α-helix	439-442	4
β-strand	448	1	31
β-strand	452-454	3	32
α-helix	460-462	3
β-strand	469	1	33
α-helix	471-472	2
β-strand	473-474	2	34
β-strand	485	1	34
β-strand	488-489	2	34
β-strand	492-494	3	32
β-strand	497	1	31
α-helix	503-505	3
β-strand	507-516	10	20
β-strand	524-525	2	30

Chain J: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	35
β-strand	11-12	2	36
β-strand	18-25	8	35
β-strand	33-39	7	37
β-strand	46-51	6	37
β-strand	58-60	3	37
β-strand	68-73	6	35
β-strand	78-83	6	35
α-helix	88-90	3
β-strand	92-99	8	37
β-strand	106-109	4	37
β-strand	113-115	3	37
β-strand	116-117	2	36
α-helix	120-122	3
β-strand	123	1	38
α-helix	124-125	2
β-strand	126-130	5	39
β-strand	142-151	10	39
β-strand	152	1	38
β-strand	157-160	4	40
α-helix	161-163	3
β-strand	169-171	3	39
α-helix	172-174	3
β-strand	175-176	2	39
β-strand	182-190	9	39
α-helix	194-197	4
β-strand	201-206	6	40
β-strand	211-216	6	40

Chain K: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	41
β-strand	10-14	5	42
β-strand	19-25	7	41
β-strand	33-38	6	42
β-strand	45-49	5	42
β-strand	53-54	2	42
α-helix	55	1
β-strand	62-67	6	41
β-strand	70-75	6	41
α-helix	80-82	3
β-strand	84-90	7	42
β-strand	94	1	16
α-helix	96	1
β-strand	97-98	2	42
β-strand	102-107	6	42
β-strand	111	1	43
α-helix	112-113	2
β-strand	114-118	5	44
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	44
β-strand	140	1	43
β-strand	145-150	6	45
β-strand	154	1	45
β-strand	159-163	5	44
α-helix	164-167	4
β-strand	173-182	10	44
α-helix	183-188	6
β-strand	191-197	7	45
β-strand	205-210	6	45

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	30-31	2	9
β-strand	36-37	2	9
β-strand	39-44	6	8
β-strand	51-55	5	8
β-strand	59-60	2	8
α-helix	61	1
β-strand	68-73	6	7
β-strand	76-81	6	7
α-helix	86-88	3
β-strand	90-96	7	8
α-helix	102	1
β-strand	103-104	2	8
β-strand	108-112	5	8
β-strand	117	1	10
β-strand	120-124	5	11
α-helix	125-127	3
α-helix	128-133	6
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-156	6	12
β-strand	159-160	2	12
α-helix	161	1
β-strand	165-169	5	11
α-helix	171-173	3
β-strand	179-188	10	11
α-helix	189-193	5
β-strand	197-203	7	12
β-strand	211-216	6	12

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain of CR3022 antibody Fab	A, H	protein	230	Homo sapiens	P01857 (AlphaFold model)
Light chain of CR3022 antibody Fab	B, L	protein	220	Homo sapiens	S6C4R6 (AlphaFold model)
Spike glycoprotein	G, I	protein	204	Pangolin coronavirus	P0DTC2 (AlphaFold model)
Heavy chain of 4C12-B12 antibody Fab	J, U	protein	230	Homo sapiens	P01857 (AlphaFold model)
Light chain of 4C12-B12 antibody Fab	K, V	protein	215	Homo sapiens	Q7Z3Y4 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>8CWJ_1 Heavy chain of CR3022 antibody Fab (chains A, H)
QMQLVQSGTEVKKPGESLKISCKGSGYGFITYWIGWVRQMPGKGLEWMGIIYPGDSETRY
SPSFQGQVTISADKSINTAYLQWSSLKASDTAIYYCAGGSGISTPMDVWGQGTTVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH

Sequence of entity 2 (B, L), FASTA

>8CWJ_2 Light chain of CR3022 antibody Fab (chains B, L)
DIQLTQSPDSLAVSLGERATINCKSSQSVLYSSINKNYLAWYQQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTPYTFGQGTKVEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (G, I), FASTA

>8CWJ_3 Spike glycoprotein (chains G, I)
TNLCPFGEVFNATTFASVYAWNRKRISNCVADYSVLYNSTSFSTFKCYGVSPTKLNDLCF
TNVYADSFVVRGDEVRQIAPGQTGRIAGYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYL
YRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFHPTNGVGYQPYRVVV
LSFELLNAPATVCGPKGSHHHHHH

Sequence of entity 4 (J, U), FASTA

>8CWJ_4 Heavy chain of 4C12-B12 antibody Fab (chains J, U)
EVQLLESGGGLVQPGGSLRLSCAASGFRISDEDMGWVRQAPGKGLEWVSYIDNAGASTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKSHYANPSFDYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH

Sequence of entity 5 (K, V), FASTA

>8CWJ_5 Light chain of 4C12-B12 antibody Fab (chains K, V)
DIQMTQSPSSLSASVGDRVTITCRASQDIADYLNWYQQKPGKAPKLLIYYASNLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQGLGMPITFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (GOL, CL) are not listed.

Primary citation

Affinity maturation endows potent activity onto class 6 SARS-CoV-2 broadly neutralizing antibodies. Mazigi, O., Langley, D.B., Henry, J.Y. et al. Proc Natl Acad Sci U S A (2025) 122:e2417544121-e2417544121. DOI 10.1073/pnas.2417544121 · PubMed

Other PDB entries of the same protein (UniProt P01857 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LLD 1.19 Å, Structure of wild-type IgG1 antibody heavy chain constant domain 1 and light chain…
3TV3 1.29 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with…
4LLQ 1.42 Å, Structure of redesigned IgG1 first constant and lambda domains (CH1:Clambda constant…
5HSF 1.52 Å, 1.52 Angstrom Crystal Structure of Fc fragment of Human IgG1.
6YT7 1.55 Å, Glycosylated knob/dummy-hole fc fragment
4NWU 1.6 Å, Crystal structure of APE1551, an anti-human NGF Fab with a nine amino acid insertion in…
1L6X 1.65 Å, Fc fragment of rituximab bound to a minimized version of the B-domain from protein A…
3TWC 1.65 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT127 in complex with…
5JIH 1.66 Å, Crystal structure of HER2 binding IgG1-Fc (Fcab STAB19)
3MCL 1.7 Å, Anti-beta-amyloid antibody c706 fab in space group P21
5U66 1.7 Å, Modified single helix from the B-domain of protein A bound to IgG1 Fc
6N35 1.75 Å, Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement

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